Jul

20

The Myelin Repair Foundation (MRF) is a non-profit medical research foundation dedicated to accelerating basic medical research into myelin repair treatments that will dramatically improve the lives of people suffering from multiple sclerosis (MS).

Jul

19

The American Medical Association recommends that physicians disclose uncertainties about the risks of implants, add extra layers of security to protect patient privacy and support ongoing research regarding the implantation of RFID devices in human beings.

July 17, 2007—The American Medical Association (AMA) has officially established a code of ethics designed to protect patients receiving RFID implants. The recommendations focus on safeguarding a patient’s privacy and health, and are the result of an evaluation by the AMA’s Council on Ethical and Judicial Affairs (CEJA) regarding the medical and ethical implications of RFID chips in humans, as well as a follow-up report recently released. The latter discusses the possible advantages and specific privacy and ethical issues of using RFID-enabled implantations for clinical purposes.

Entitled “Radio Frequency ID Devices in Humans,” the report is presented by Robert M. Sade, M.D., who chairs the CEJA. It acknowledges that RFID’s use in health care “represents another promising development in information technology, but also raises important ethical, legal and social issues.” The report adds, “Specifically, the use of RFID labeling in humans for medical purposes may improve patient safety, but also may pose some physical risks, compromise patient privacy, or present other social hazards.”

The AMA’s report identifies three specific recommendations: The informed-consent process must include disclosure of medical uncertainties associated with these devices; physicians should strive to protect patients’ privacy by storing confidential information only on RFID devices utilizing informational security similar to that required for medical records; and physicians should support research into the safety and efficacy of RFID devices implanted in human beings, and examine the role of doctors regarding the nonmedical uses of the technology.

The recommendations now serve as ethical guidelines for physicians and caregivers, explains Steven Stack, M.D., a member of the AMA’s board of trustees, and are officially part of the AMA’s medical ethics code. While not law, the AMA’s code of ethics has long served as a standard of conduct defining the essentials of honorable physician behavior.

“The AMA is the largest professional organization representing the interest of physicians and patients in the U.S.,” Stack says, “and the AMA’s code of ethics is the most widely accepted guidance for physicians’ professional, ethical practices.” In fact, he adds, courts and governments often use the AMA’s ethics codes as guidelines.

Central to the AMA’s recommendations is that RFID implantable devices still need to be researched. The report indicates such implants may present physical risks to patients, because the devices can migrate under the skin and become difficult to extract. It goes on to say the risks may be minimized “by constructing RFID tags from materials that permit surrounding tissue to encase the device.” Furthermore, the document cautions that RFID tags may electromagnetically interfere with electrosurgical devices (medical tools that use electrical currents for cauterization during surgery) and defibrillators, and that more research needs to be done regarding whether RFID tags might also affect the efficacy of pharmaceuticals.

From a privacy perspective, the AMA notes, RFID device security has not been fully established, so physicians “cannot assure patients that the personal information contained on RFID tags will be appropriately protected.” Beyond just storing unique ID numbers on the tags, the association suggests the medical community also consider computer encryption and digital signatures to protect the data.

Moreover, the report recommends that RFID tags not be implanted or removed without the prior consent of patients, as per the AMA’s policies regarding informed consent. More specifically, patients—or those acting as the legal guardians of patients—should be informed of the potential risks and benefits associated with RFID tags, as well as who will be granted access to the data contained on those tags, and the purposes for which this information will be used.

Shortly after the AMA released its report, VeriChip Corp., a maker of implantable RFID tags, applauded the association’srecommendations, saying they could help improve the acceptance of RFID implantable devices in the health-care industry. VeriChip manufactures the VeriMed system, which features a glass-encased passive RFID tag that can be injected into a patient’s arm.

A hospital or medical staffer carrying a handheld interrogator can read a VeriChip’s unique 16-digit identifying number, then link that patient’s identity to such medical-record details as allergies, medications taken and blood type. The VeriMed system is the only human-implantable radio frequency transponder system cleared by the U.S. Food and Drug Administration (FDA) for the purpose of patient identification and health information.

VeriChip could not be reached by press time to comment on some of the AMA’s concerns regarding RF interference, privacy and security. In the past, however, the company has claimed that when its glass-encased tag is inserted just under the skin, a small amount of scar tissue forms around it, preventing the chip from moving or migrating. In addition, VeriChip has stated that any patient data associated with the 16-digit number is stored in a secure online database, accessible only by authorized health-care workers.

Jul

19

Stewart Brand is a cofounder of Global Business Network and the Long Now Foundation. Best known for founding, editing, and publishing the Whole Earth Catalog (1968-1985; National Book Award, 1972), he also has a long-standing involvement in computers, education, and the media arts.

From 1987 to 1989 Stewart ran a series of private conferences on “Learning in Complex Systems,” sponsored by strategic planners at Royal Dutch/Shell, AT&T, and Volvo. In 1988 he joined the Board of Trustees of the Santa Fe Institute, an organization dedicated to multi-disciplinary research in the sciences of complexity. In 1987, Stewart wrote The Media Lab: Inventing the Future at MIT (Viking). It became a QPB Selection, won the Eliot Montroll Award, and has been translated into Japanese, German, Italian, and Spanish. From 1974 to 1985, Stewart founded, edited, and published CoEvolution Quarterly. He also served as editor-in-chief of the Whole Earth Software Catalog (Doubleday) from 1983-1985. During this time, Brand organized the first “Hackers’ Conference,” which was televised nationally and has since become an annual event. He also founded The WELL (Whole Earth ‘Lectronic Link) a computer teleconference based in the San Francisco Bay Area. It now has 10,000 active users, and is considered a bellwether of the medium.

After receiving his degree in biology from Stanford in 1960 and spending two years as a US Infantry officer, Stewart became a photojournalist and multimedia artist, performing at colleges and museums. In 1968, he was a consultant to Douglas Engelbart’s pioneering Augmented Human Intellect program at SRI, which devised now-familiar computer interface tools. In 1972, for Rolling Stone, he wrote the first article about the computer lifestyle, entitled “Fanatic Life and Symbolic Death Among the Computer Bums,” chronicling the fringes of computer science at Xerox PARC, the Stanford Artificial Intelligence Laboratory, and MIT. That article became part of his book, Two Cybernetic Frontiers (Random House, 1974), which also introduced anthropologist/ philosopher Gregory Bateson to a wide audience. In 1974 he organized a “New Games Tournament,” which generated three books and became a genre in experiential education.

In 1994, eight years of research by Stewart into how buildings change over time (a form of organizational learning) came together in a richly illustrated book, How Buildings Learn: What Happens After They’re Built. Referred to as “a classic and possibly a work of genius,” the book has been used as a text by computer systems designers as well as building preservers, architects, and many lay building users.

Since co-founding The Long Now Foundation with Danny Hillis in 1996, Stewart has been involved with its growing number of projects. The 10,000-year Clock project aims to build a monumental timepiece inside a mountain in eastern Nevada; the first working prototype went on permanent display at the Science Museum in London. The Rosetta Project set about micro-etching 1,000 languages on a 3-inch nickel disk and wound up building the world’s largest website of living languages. Long Bets is another web project, this one to make a permanent repository and forum for “accountable predictions,” where each Prediction accumulates votes and discussion and can become a bet with real money at stake. The All Species Inventory was spun off as its own foundation, with the aim of discovering and cataloging every life form on earth within the current human generation. Another project, called Long Server, is attempting to help solve the very difficult problems in long-term preservation of digital materials. Stewart’s book, The Clock of the Long Now: Time and Responsibility, investigates the advantages of taking the very long term seriously, including some new ways to think about the future.

Jul

17

Many centuries ago, farmers in China first tried the sensible idea of using natural predators to control crop pests. Today, Dr. Zhao Jingzhao, President of the University of Hubei, renews the promise of this ancient technique. He has made tremendous advances with biological control which are setting examples for other countries.The farmers Zhao works with combine this technique with a very modest use of chemical pesticides. That combination is known as integrated pest management.

China is the world’s biggest producer of cotton, and cotton is the chief crop in Hubei Province. People who work in the cotton fields of Hubei Province once relied solely on pesticides. But even as they spent more and more money on them, they saw their harvests dwindle, and that chemicals could make you ill.

Zhao set about to help those farmers. To do so, he has dedicated more than ten years of his life to studying various means of biological pest control.

Nearly two thousand years ago, in the orange groves of China, farmers came up with a new way to do battle with insect pests. Beetles, mites, and stinkbugs plagued their trees. Farmers would release ants among the trees, and the ants would dine on the uninvited guests. The farmers knew which species of ants to use – how to breed the ants – and the ideal tie of year to put them to work.

Today, near Wuhan on the Yangtse River, 1,000 kilometers south of Beijing, Dr. Zhao Jingzhao is continuing this tradition by finding ways to control cotton pests with their natural enemies. Cotton has posed difficulties to its growers for hundreds of years – in China, in the United States, and in other countries.

Spiders work better than pesticides

In China, the main cotton pest is the boll weevil – also a danger to cotton crops in other countries. Zhao’s efforts to perfect new methods of biological control have a certain urgency, because farmers and scientists are increasingly troubled by the costs and dangers of chemicals pesticide use.

Fifteen years ago Zhao turned his attention from rice cultivation to cotton in an effort to reduce the use of chemicals and to stop the poisoning of the environment. Spiders, he found, were the best answer. He conducted a nationwide survey analyzing the range of different spiders active in cotton fields. Rice paddies, fruit trees and corn fields were also studied. In looking for natural predators to control cotton pests, Dr. Zhao found that of 600 predators, more than 100 were varieties of spiders.

After Dr. Zhao and his colleagues select the best spider for a given region and a given pest, they then face the challenge of finding ways to maintain the population.
In Zhao’s words:

“In Hubei Province, cotton is planted after the wheat harvest. During the harvest, and in the winter, we dig shallow holes and fill them with grass, and we also put grass among the branches of plants. The spiders stay in these grassy areas. This is a simple way to secure a healthy supply of spiders. Then, when the cotton blooms, they come out and eat the pests.”

Zhao is helping a new generation of Chinese farmers rediscover the merits of biological control. By setting the spiders loose in their fields, the farmers find that their crop yields increase. At the same time, they have cut down on chemical use by 80%.

The success that Zhao and his colleagues have had with natural pest control places their expertise in high demand. The United States is one of the countries with whom they exchange ideas.

Biological control began twenty centuries ago in China, but just one century ago in the United States. In 1889, California orange growers were losing their crops to a bug known as the cottony cushion scale. They successfully responded by enlisting the help of a small but hungry insect recently arrived from Australia, the seven-spotted ladybug.

In California’s San Joaqiun valley, as in Hubei, changes from pesticide dependence are underway.

California grows half the fruits and vegetables in the United States. Its farmers handle a lot of dangerous pesticides. One of the chemicals, parathion, has been used heavily on cotton and food crops. Parathion has killed more than fifty farm workers who have handled it. By drifting through the air or collecting in groundwater, it has poisoned many more people, with less-than-fatal, but nonetheless serious consequences. The risks of pesticides – on and off the farm, to children and to adults – have lead many farmers in the San Joaquin valley to turn to organic farming and to biological control. The movements toward integrated pest management are fraught with opposing opinions, but changes are nonetheless underway.

Farming practices in California are changing. In 1984, only 4,000 acres were entirely organic, with no pesticides at all. That number was up to 70,000 by 1990, and many more are under integrated pest management.

One difficult associated with integrated pest management is the cost of providing a continuous diet for the predators, when supplies of pests fall. In California and at the Department of Agriculture, work is underway to develop artificial diets for the beneficial insects, although thus far with limited success. In China, Dr. Zhao spent several years developing such a diet for spiders. He tried dozens of ingredients before he found a combination that worked. The ingredients are simple – egg, honey, sugar, several vitamins and enzymes, milk powder, and water.

Zhao encourages farmers to think of a farm, not as a short-term factory that produces a single annual product, but rather as part of a diverse ecosystem that has to be there for the long haul. He stresses the importance of planting a variety of crops rather than just one, that it is crucial to preserve and use a variety of seeds, and that it’s the ecologically healthy, balanced agricultural system that works.

Farmers in other parts of China, inspired by Zhao’s success, are applying integrated pest management to cotton and to other crops as well. Zhao’s discovery of a successful natural means of controlling the boll weevil, a centuries’ old problem, can now benefit cotton growers not only in China, but in other countries as well. Cotton farmers throughout Hubei now use fewer pesticides, yet produce bigger crops. Their standard of living is improving. They now spend less money on pesticides and make more from their crops, and they have fewer health problems, when Spiders, not pesticides, benefit China’s farming

Health dangers and pest resistance associated with pesticide use in agriculture.

Worldwide, about a million people are poisoned by pesticides each year; ten thousand of these victims die from such poisonings. The risks are greatest in developing countries. Ninety-nine percent of the deaths caused by agricultural chemicals occur in those countries.

Many farm workers cannot read the warning labels about careful use, because they do not know how to read or because the label is in a foreign language. The farmers may be totally unaware of the dangers of handling these chemicals. Often they don’t know that they should avoid reusing pesticide containers for food or water. And when they do understand the warnings, they often don’t have protective clothing or proper storage facilities.

Chemical pesticides have helped millions of people, yet are a mixed blessing. In 1958, the World Health Organization intensified the efforts to eradicate malaria. The insecticide DDT was found to kill the malaria-causing mosquitoes and the incidence of malaria fell dramatically.

Then suddenly, after only five years of spraying, the momentum reversed. Every two years the number of people suffering from malaria doubled. The mosquitoes had developed a resistance to DDT.

The startling realization of how quickly and effectively mosquitoes develop resistance to chemical control was to be seen again and again in the attempts to control insects – both those carrying disease and those plaguing farmers’ crops. The malaria story – an intensive pesticide campaign followed by new generations of pests who outlive any attempt to kill them – by now is a familiar one. It’s happened in efforts to wipe out insects that carry diseases, and it’s happened when farmers have tried to rid their fields of pests.

Nearly 25% of the world’s pesticides are used on cotton – in the United States nearly 50%. But despite this massive bombardment with chemicals, yields are declining in much of the world. In the United States, cotton growers in Texas and other states gave up vast acreage of cotton when pesticides became to costly and ineffective. With chemical dependence, shrinking yields, and decreasing income from crops, the agricultural picture is too often a grim one.

The recent disappearance, world-wide, of honey bees, may be due to the toxins in pesticides, which are used for many crops, pollinated by the honeybees.

Thinking Green

Think of a farm, not as a short-term factory that produces a single annual product, but rather as part of a diverse ecosystem that has to be there for the long haul. Understand, the importance of planting a variety of crops rather than just one; and, it is crucial to preserve and use a variety of seeds. Biological research shows that the ecologically healthy, balanced agricultural system is what works.

Jul

16

The discovery that zebrafish produce natural chemicals that enhance production of blood-forming stem cells may translate rapidly into new treatments to increase the success of bone marrow or cord blood transplants in humans.

The research team, which was led by Leonard Zon, a Howard Hughes Medical Institute researcher at Children’s Hospital in Boston, published its findings in the June 21, 2007, issue of the journal Nature. Trista North, a postdoctoral fellow in Zon’s laboratory, was lead author.

In their experiments, the researchers were searching for compounds that would increase the production of blood-forming, or hematopoietic, stem cells (HSCs). Zon said that such compounds could be clinically important in enhancing success of bone marrow and cord blood transplantation. One of the aims of bone marrow transplantation is to restore the immune systems of patients whose blood cells have been depleted by cancer therapy.

“In earlier work, we developed staining methods that marked HSCs in the developing zebrafish embryo,” said Zon. “Since we can produce and test thousands of zebrafish embryos at a time, we have a very quick and efficient model for large-scale testing. So, Trista and I came up with the idea of conducting a mass screening of chemicals from a library to see whether we could find any that increased the quantity of stem cells.”

The researchers screened a library of 2,275 chemicals, about a third of which are already FDA-approved, said Zon. They began by placing fish embryos in the tiny wells of a culture dish. Once the embryos were in place, the researchers added one of the chemicals, stained the embryos for stem cells, and observed whether the chemical enhanced or decreased stem cell production.

The scientists identified 35 compounds that increased HSC production and 47 that decreased it. The result of the screening also yielded an important discovery about the regulatory mechanism for stem cells, said Zon.

“When we looked at the list of chemicals that affected stem cells, what was staring us in the face was that many acted on the prostaglandin regulatory pathway,” said Zon. “This prompted us to explore this pathway in more depth.” Prostaglandins are fatty hormone-like chemicals known to regulate a wide array of body processes.

Further exploration revealed that the prostaglandin E2 (PGE2) in the zebrafish played a central role in regulating HSC formation. When they administered a long-acting version of PGE2 to fish embryos, they saw a considerable enhancement of stem cell production.

In additional studies with both adult zebrafish and mice, they found that the long-acting PGE2 greatly enhanced HSC production. Conversely, inhibiting PGE2 diminished HSC production. In particular, when they transplanted both PGE2-treated and untreated stem cells into mice, the treated cells far outperformed the untreated cells in their ability to proliferate.

The researchers also found that decreasing expression of two regulators of PGE2—cox 1 and cox 2—also decreased stem cell production. This finding is important for human bone marrow recipients, because pain medications such as aspirin and ibuprofen are cox inhibitors, said Zon.

While the HSC-enhancing drugs they identified could find use in aiding marrow transplantation, they will likely be especially important in cord blood transplantation, said Zon. In this treatment, stem cells from umbilical cord blood are transplanted to restore the immune system in immune-compromised patients.

“Cord blood has a limited number of stem cells in it, enough so that the blood from a single cord is sufficient for a small child. However, when it is transplanted into an adult, there is a 40 percent chance that the patient won’t engraft, because there aren’t enough stem cells in the sample,” said Zon. “When adult patients are given two cords from unrelated donors, this chance of failure is reduced, but there may be immunological problems from interaction between the two sources.

“Using drugs that enhance PGE2 to amplify the number of stem cells in a cord sample could enable use of only one cord in such patients,” said Zon. “And it may even help patients who don’t engraft.” Zon said he and his colleagues plan to begin clinical trials of such HSC-enhancement using the long-acting version of PGE2.

Jul

14

It can take hours, or even days, for a virus to infect a cell. But poliovirus is more efficient than the average virus, new research has shown. Once inside its host cell, poliovirus needs only minutes to release its genome and initiate an infection.

Using fluorescence microscopy to watch as individual polioviruses entered host cells, Howard Hughes Medical Institute researchers at Harvard University have found that the virus must be internalized into a cell in order to release its genome, but once inside, genome release is quick and efficient, and takes place near the cell membrane.

The results, 07/2007, in the journal Public Library of Science Biology, not only have implications for the understanding of basic virology, but also established a novel method for studying viral entry. Despite decades of studying poliovirus, researchers still didn’t fully understand how it infected cells. There was a debate about whether this virus releases its RNA right at the cell surface or whether it needs to be internalized first.

One reason for the debate was that while several hundreds of poliovirus particles may attempt to invade a host cell, few of these actually lead to infection. “You would worry about following a large number of virus particles that turn out to be non-infective,” Dr. Zhuang noted. “Then everything you discovered about how they get into the cell is irrelevant.”

James Hogle, a specialist on polioviruses, added, “Without a proper research design, you never know if you’re looking at an infective pathway or not.” To overcome this obstacle, the researchers combined studies of viruses’ ability to infect cells with sensitive live cell microscopy techniques that allowed them to track individual polioviruses, each one a thousand times smaller than the cell it infiltrates.

Because they wanted to see how intact poliovirus enters cells, as well as how it releases its genetic material once inside, they tagged the viruses with two different fluorescent dyes. The first bound to RNA, the genetic material carried by polioviruses, and caused it to glow green. The researchers took care to choose an RNA-binding dye that would not interfere with the infectivity of the virus.

They used a different dye to label the protective outer coat of the virus, known as the capsid. They labeled the capsids with a dye that fluoresced in red. In some experiments, the investigators chose a pH-sensitive red dye that fluoresces only at neutral or acidic pH (7 or lower). This way, when the extra-cellular environment was briefly raised to a higher pH, the viruses became invisible. Once a virus entered a host cell, however, the dye would constantly emit red fluorescence, because cells and intracellular organelles typically maintain a pH close to or below 7. Using this approach, the researchers could unambiguously tell whether a virus particle had been internalized into a cell.

Through the microscope, the researchers watched as polioviruses entered host cells, emitting both red and green light, and then released their green-hued RNA. They could see that the virus enters cells through endocytosis, a process in which the cell membrane folds around the virus and creates a sac inside the cell. And by correlating this observation with studies of infectivity, Zhuang said, “We settled the debate. We found that the virus does require endocytosis. If the viruses don’t get into the cell, they do not release their RNA.”

The group also found that viral RNA was released almost immediately after a virus particle entered the cell. “Seventy-five percent of polioviruses release their RNA genome in the first 30 minutes,” said Boerries Brandenburg, a postdoctoral researcher in Zhuang’s lab and first author of the paper.

“We found that polio’s genome release is efficient,” he said. “That’s not the limiting mechanism of infectivity. There were previous suggestions that it might be.”

The group also examined the effects of multiple drugs against the infectivity of the virus. They found that the virus doesn’t use any of the known endocytosis pathways to get inside a cell.

“We’re not the first group to use drugs to test which cellular mechanisms are involved in infection,” said Brandenburg. “But it’s sometimes difficult to find out whether the drugs are affecting infection, or just negatively affecting the cell. Likewise, problems also exist for single-virus tracking experiments in live cells. It is not easy to tell whether the viruses being tracked are the ones that lead to infection. We spent a lot of time on both assays to make sure that our observations are relevant to infection.”

Jul

13

The energy giant has become the biggest investor in some of the most out-there genetics research.

Oil companies are better known for burning fossil fuels than splicing genes. But BP, the energy giant formerly known as British Petroleum, has made leading-edge technologies like custom engineered bacteria a linchpin of its strategy to face up to global warming.

In the process, germs would be souped up to make ethanol, biobutanol or other fuels from plants like corn. Scientists would embed the genomes of bacteria with genes taken from termites, sheep guts or microbes that live on your lawn. The very plants they consumed would also be bioengineered, and even more re-engineered bacteria might produce gasoline or similar fuels directly.

Still more newly discovered microbes that live in oil or natural gas wells might increase the efficiency of existing drilling and mining. Our economy is based on fossil fuels, the remains of long dead organisms. But in the future we might rely on life forms that have never before existed. BP declined to comment directly on its biotech strategy.

“BP is not doing this because they want to fund basic research,” says Aristides Patrinos, the former director of the Office of Biological and Environmental Research and now president of biotech startup Synthetic Genomics. “This revolution in biology is ushering in new tools that, by revisiting old tricks, can make energy production a lot more effective.”

The most prominent bet being made by BP is a plan to spend $500 million over 10 years to fund the Energy Biosciences Institute (EBI), a proposed laboratory at the University of California, Berkeley. The neighboring Lawrence Berkeley National Laboratories and the University of Illinois, Urbana-Champaign are also involved in the project. The project will look at bioscience approaches from agriculture to economics, and will also study the ethical implications of all this new biotech work.

But already, before the institute is built or the contract even signed, the EBI is drawing controversy on the Berkeley campus.

One worry is that the new science of synthetic biology, the souped-up form of genetic engineering that involves radically modifying organisms or even someday designing them from scratch, is both more promising and more dangerous that the technology that has been around for two decades and gave birth to Amgen, Genencor, and Monsanto. Another concern is that BP will get significant intellectual property rights to the work being done at Berkeley, including the right of first refusal to a flood of IP that could result.

But perhaps the biggest red flag is the potential for conflict of interest, as a small number of researchers look to start up what could be a big new research field for academics and industry alike.

Chris Somerville, the Stanford plant geneticist who has been tapped to run the big project, is himself the co-founder of two biotech firms that will work in the same field as the institute. In one, the plant biotech startup Mendel Biotechnology, he has a significant interest, he says; he has less interest in the second, a biofuel startup called LS9.

Somerville has given up any control in either and is in compliance with Berkeley’s conflict of interest policies. But he says he cannot afford to give up his stakes in the companies; they would be difficult to trade at a fair value because the firms are not public.

But the connections don’t end there. Mendel also has a deal with BP, as does another biofuels play, Amyris Biotechnologies, which was founded by Jay Keasling, a Berkeley synthetic biology whiz who initially sought to make cheaper malaria medicines. (That effort got him a $43 million grant from the Bill and Melinda Gates Foundation.) But now Amyris is in the biofuels biz. John G. Melo, the former head of BP’s biofuels unit, is its chief executive.

Synthetic biology is such a small field right now that Keasling and Somerville were both initially involved with LS9, but left, leaving Harvard researcher George Church as the main scientific founder. Now Church says that LS9 is making significant progress, engineering E. coli to produce hydrocarbons. The idea is that bacteria could somehow efficiently make fuels that resemble gasoline, but with fewer environmental costs.

“These things don’t get immediately disentangled,” says Church, who worked in the medical biotech business as a researcher in the early days of Biogen, now part of Biogen Idec, before coming to Harvard. “In any meteorically rising field, the number of people is going to be small, and they’re competing against each other at a commercial and academic level.”

Another company that has a deal with BP is Synthetic Genomics, which was founded by human genome pioneer J. Craig Venter. The firm recently made headlines by showing that the genome of one bacteria species could be transplanted into a similar one–a step toward making a germ with entirely man-made genes.

But the company’s tie-up with BP focuses on another area: using the sequencing technologies that Venter has pioneered to examine the microbes that are found inside natural gas and oil wells. Jonathan Eisen, a researcher at UC-Davis who is not working on the project, says that although that might not produce new kinds of fuels, these undiscovered species could make the discovery of existing fuels more efficient.

Venter says the goal is to discover the “thousands and thousands” of different organisms found in fossil fuel sites, from coal beds to oil wells.

These environments are super-hot, and exactly what kinds of microbes live in them is basically unknown. Patrinos helped launch efforts to learn how to collect living things from such otherworldly environments while he was at the DOE.

Just because BP is being so public about its research by investing in biotech firms and academics doesn’t mean its rivals aren’t quietly making their own investments. Chevron, for instance, formed a biofuels business unit last May. One disadvantage to BP’s approach is that university researchers won’t keep their work secret, as in-house scientists might.

In the past, biotech has never succeeded in areas like mining or manufacturing in the same way it did in medicine. Now, with new technologies that allow scientists to find and alter microbes in ways that were never before possible, a new generation of biologists is looking to change that.

And BP is funding them.

Jul

12

Juggling Genetics
Matthew Herper
Forbes.com
J Craig Venter secured his place in the scientific firmament seven years ago when he nearly outran the U.S. government in the race to map the human genome. He’s aiming impossibly high again, making big headlines for transplanting the entire genome of one species of bacterium into another. It was hailed by several scientists as a step toward producing the first man-made organism that, according to Venter, could as soon as five years from now help solve global warming by reducing our reliance on fossil fuels.

Venter’s transplanting trick was another wow moment at his 500-person gene machine, which goes by an easy-to-remember name, the J. Craig Venter Institute. Its $200 million in assets is funded in part by gains from his biotech business ventures. Venter, 60, is one of the two most mentioned researchers in a recent textbook on recombinant DNA.

Being the Bono of genetics allows him to fund audacious ideas that might otherwise be starved of support, but here’s the thing to know about Venter: He warps the reality field around genetic research through sheer force of ego and showmanship. Lots of researchers are already crafting synthetic organisms by modifying the genes of existing germs, but Venter is going for an entirely man-made organism. It’s a huge, stupendous goal, but he’s also using the smallest and most fragile bacteria around. Lots of researchers have been decoding the genes of rare microbes, but only Venter did it by scooping up gallons of seawater from the deck of his 100-foot yacht. Venter was the first to precisely map an entire human genome. It was put up on the Internet in May and will be published soon. Guess whose genome it is? Venter’s. His autobiography is due out in October. It’s called A Life Decoded: My Genome: My Life.

Venter’s Great Man act might frustrate those who like their science with a dose of modesty or circumspection. Nobel laureate Hamilton Smith does much of the hard work at Venter’s institute. Venter has publicly credited Smith, but have you heard of him? Venter “makes good copy, I guess,” says Mark Adams, a Case Western Reserve geneticist who was one of Venter’s lieutenants for a decade.

That big ego has left in its wake chaos and bitter feelings. At Venter’s former genetics lab, the not-for-profit Institute for Genomic Research, managers battled over control of grant money and equipment while his 23-year marriage to renowned genomic scientist Claire Fraser (who ran the place) fell apart. Of the 28 highest-ranking scientists, 23 departed, mostly for better jobs. What’s left of the institution (referred to everywhere as TIGR, like the predator) has been consumed by his new Venter Institute.

Venter declined comment for this story, but Venter Institute spokeswoman Heather Kowalski (also his fianc??e) says that scientists switch jobs all the time. Venter, she says, “is a strong personality, someone who has strong opinions and someone who pursues his ideas with steadfast determination. While it’s clear he has his detractors, he’s also got plenty of admirers.”

Venter founded TIGR in 1992 after leaving the National Institutes of Health for complicated reasons that included a front-page controversy over patenting genes. At the NIH Venter was busily discovering brain genes, and the NIH wanted to patent them even before knowing what the genes did. W. Richard McCombie, a lab mate of Venter’s who is now a Cold Spring Harbor Laboratory professor, remembers Venter walking into the lab after the NIH decision and saying, “We’re going to be rich and powerful beyond our imagination.” (Another lab mate also remembers the quote, but Kowalski disputes it as a selective memory from a disgruntled ex-employee.) Almost immediately, a slew of critics railed against privatizing genes. Venter has since come out against broad gene patents.

The NIH ended up quashing the gene-patenting idea, but Venter’s work brought him to the attention of Wallace Steinberg, a venture capitalist who wanted Venter’s know-how for a startup he had in mind. Venter had another idea. He would license new genes to Steinberg’s firm but only via an institute Steinberg would bankroll: TIGR. Venter and Fraser left for the new institute in Rockville, Md. There they sequenced the very first genomes, of two different bacteria, in 1995.

Three years later Venter jumped at the chance for the big job, sequencing the entire human genome, at the biotech Celera. He took a select group of TIGR’s best and brightest with him, creating hurt feelings among those left behind.

TIGR researchers had worked in lockstep behind Venter. But Fraser nurtured a more independent approach, akin to that of a university faculty. TIGR thrived and developed a reputation for understanding the genes of scary germs. It sequenced the malaria genome and the anthrax strain that was unleashed in Washington, D.C. and New York in 2001. Work began on a big project to understand potential flu pandemic threats.

Even as Venter was triumphing over the government’s gene-mappers in 2000, stock in Celera plummeted as it dawned on investors that the company would have trouble turning DNA data into cash. Venter was fired in 2002 in a dispute over Celera’s future. He returned to the TIGR campus with big plans.

He created three new not-for-profits. One would focus on genomics; a second would do synthetic biology for energy production; and the third would serve as a funding mechanism for the two new organizations and TIGR. Gene-sequencing machines, the workhorses at TIGR, were now to be shared by all at a new 40,000-square-foot facility.

Venter and Fraser began to tussle over the direction of TIGR, and they separated in 2004. That September Venter went to the boards of TIGR and the other not-for-profits with a plan to merge them into a single J. Craig Venter Institute. Virtually all 28 of TIGR’s faculty threatened to quit. “I for one was not willing to work at a place called the J. Craig Venter Institute,” says Steven Salzberg, a TIGR researcher who has since left for the University of Maryland. The other institutes did merge, but TIGR was left separate and withering.

Venter and Fraser divorced in February 2005, but they continued to work closely together. That June Fraser married geneticist Stephen B. Liggett and changed her last name to Fraser-Liggett. By 2006 Venter was dating Kowalski, who had been the publicist at Celera.

In 2006 Venter finally got his wish to absorb TIGR into the J. Craig Venter Institute. Fraser-Liggett fought behind the scenes to slow down the move, arguing that the tumult was driving away her faculty. “If too many more people leave, then the stench of death will start to permeate this organization,” Fraser-Liggett wrote in a memo to the TIGR faculty.

In April Fraser-Liggett left the Venter Institute to start a new genomics research organization at the University of Maryland School of Medicine. Ten of her TIGR colleagues are following as full-time faculty members, and most of their staff are coming, too. This institute will use new gene-sequencing machines to study how infectious germs behave and evolve inside the body. It will employ 100 people and will open this fall.